de.sekmi.histream.i2b2

Class I2b2ExtractorFactory

java.lang.Object

de.sekmi.histream.i2b2.I2b2ExtractorFactory

All Implemented Interfaces:

ObservationExtractor, AutoCloseable

public class I2b2ExtractorFactory
extends Object
implements AutoCloseable, ObservationExtractor

Extract observations from i2b2.

Allows simple queries against the i2b2 observation_fact table and retrieval of facts.

TODO add/use interface from histream-core

Author:

R.W.Majeed

Field Summary

Fields

Modifier and Type	Field and Description
static String	ALLOW_WILDCARD_CONCEPT_CODES Boolean feature whether to allow wildcard concept keys.

Constructor Summary

Constructors

Constructor and Description
I2b2ExtractorFactory(DataSource crc_ds, ObservationFactory factory)

Method Summary

Modifier and Type	Method and Description
void	close()
ObservationSupplier	extract(Instant start_min, Instant start_max, Iterable<String> notations)
protected I2b2Extractor	extract(Timestamp start_min, Timestamp start_max, Iterable<String> notations) Extract observations for given concept codes with observation.start between start_min and start_end.
ObservationFactory	getObservationFactory()
PreparedStatement	prepareStatement(Connection dbc, String sql)
void	setFeature(String feature, Object value)
void	setProperty(String property, Object value)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ALLOW_WILDCARD_CONCEPT_CODES

public static String ALLOW_WILDCARD_CONCEPT_CODES

Boolean feature whether to allow wildcard concept keys.

Use with caution: Unexpected results might happen if wildcard concepts overlap. (Such as query fails, duplicate facts, etc.)

Constructor Detail

I2b2ExtractorFactory

public I2b2ExtractorFactory(DataSource crc_ds,
                            ObservationFactory factory)
                     throws SQLException

Throws:

SQLException

Method Detail

getObservationFactory

public ObservationFactory getObservationFactory()

setFeature

public void setFeature(String feature,
                       Object value)

prepareStatement

public PreparedStatement prepareStatement(Connection dbc,
                                          String sql)
                                   throws SQLException

Throws:

SQLException

setProperty

public void setProperty(String property,
                        Object value)

extract

protected I2b2Extractor extract(Timestamp start_min,
                                Timestamp start_max,
                                Iterable<String> notations)
                         throws SQLException

Extract observations for given concept codes with observation.start between start_min and start_end.

The query can use the index of_idx_clusteredconcept for concept_cd and of_idx_start_date for start_date.

TODO integration test without concepts, with normal concepts, with wildcard concepts, wildcard concepts with literal _ or % in id

Parameters:

start_min - start date of returned observations must be greater than start_min

start_max - start date of returned observations must be less than start_max

notations - concept ids to extract

Returns:

extractor

Throws:

SQLException - error

close

public void close()
           throws SQLException

Specified by:

close in interface AutoCloseable

Throws:

SQLException

extract

public ObservationSupplier extract(Instant start_min,
                                   Instant start_max,
                                   Iterable<String> notations)
                            throws ObservationException

Specified by:

extract in interface ObservationExtractor

Throws:

ObservationException